World’s Smallest Genome

| 61 Comments

It clocks in at just under 160 kilobases. To put that into perspective, the human genome is over 3 gigabases.

And it has all of 182 genes.

How small can a genome get and still run a living organism? Researchers now say that a symbiotic bacterium called Carsonella ruddii, which lives off sap-feeding insects, has taken the record for smallest genome with just 159,662 ‘letters’ (or base pairs) of DNA and 182 protein-coding genes. At one-third the size of previously found ‘minimal’ organisms, it is smaller than researchers thought they would find. […]

This is encouraging news for synthetic biologists who are hoping to make designer bacteria from scratch, which could perform useful functions such as synthesizing pharmaceuticals or fuels.

Sounds like fun. And this discovery gives us some insights into the evolution of larger, eukaryotic cells as well:

C. ruddii seems even more extreme. “Its gene inventory seems insufficient for most biological processes that appear to be essential for bacterial life,” write Atsushi Nakabachi at the University of Arizona in Tucson, Masahira Hattori at the University of Tokyo, Japan, and their colleagues. At the moment, the researchers are not sure how C. ruddii copes, although they speculate that some of the necessary genes may have been transferred over evolutionary time to the genomes of the host.

That is precisely what is thought to have happened during the evolution of the compartments called mitochondria in our own cells, which are responsible for energy production. These are believed to have once been symbionts that lost all autonomy by relinquishing most of their genes to the host (mitochondria still have their own DNA).

Andersson says that C. ruddii might be analogues of mitochondria, caught in the process of changing from separate but dependent organisms into structures that will be engulfed and incorporated into the host cells.

In spite of the fact that creationists like to bring up the hypothesized endosymbiosis of mitochondria or chloroplasts as a problem for evolution, the fact is that we find intermediates between fully autonomous prokaryotes and full endosymbionts all over nature. (My favorite example is Wolbachia.) It appears that they go through an intracellular parasitic stage and, like with many parasitic relationships, both the parasite and the host evolve to cope with each other. In the case of endosymbionts, they become increasingly more cooperative until they become inseparable.

61 Comments

Foolish EVILutionist. This proves creationism. Since there is no organism with 183 genes, it is a clearly unbridgeable gap that you cannot fill.

Pretty cool, I’ve seen transcripts that are longer than that. Take Ebf1, whose unspliced transcript clocks in at just under 390 kb.

Entertainingly, the largest (known) virus has 900 genes and 800 kb of DNA: http://www.newscientist.com/article.ns?id=dn3559

“Variation within the kind”, I expect.

After I read this paper I made a bet with a friend whether it would be idthefuture or uncommondescent who will be the first to claim that this proves abiogenesis must involve 180 genes forming simeltaneously from random nucleotides and is therefore too improbable.

At the moment, the researchers are not sure how C. ruddii copes,…

So it’s not capable of feeding/reproducing itself?

After I read this paper I made a bet with a friend whether it would be idthefuture or uncommondescent who will be the first to claim that this proves abiogenesis must involve 180 genes forming simeltaneously from random nucleotides and is therefore too improbable.

I have seen creos argue before that the size of the smallest known genome (which at the time I saw this claim was over 300 genes) meant that the first organism had to have at least this many genes. My reply was, what makes you think this is really the smallest possible genome?

So it’s not capable of feeding/reproducing itself?

Of course it is. Saying that we don’t know how it copes it isn’t the same as saying that it can’t. If it couldn’t feed or reproduce, it wouldn’t be here for us to marvel at.

How small can a genome get and still run a living organism? Researchers now say that a symbiotic bacterium called Carsonella ruddii, which lives off sap-feeding insects, has taken the record for smallest genome with just 159,662 ‘letters’ (or base pairs) of DNA and 182 protein-coding genes.

So how many of the 159,662 bp are “junk”?

So how many of the 159,662 bp are “junk”?

Very little I expect, large amounts of “junk” DNA are mostly found in eukaryotes. Google on “c-value paradox”.

Andersson says that C. ruddii might be analogues of mitochondria, caught in the process of changing from separate but dependent organisms into structures that will be engulfed and incorporated into the host cells.

Ok, just for kicks, what are the average number of base pairs in mitochondria that have been sampled so far?

aren’t human mtDNA strands around 16K?

Ok, just for kicks, what are the average number of base pairs in mitochondria that have been sampled so far?

Mitochondrial DNA is very short indeed, but let us not forget that many mitochondrial proteins are encoded by the nuclear genome.

So it’s not capable of feeding/reproducing itself?

Of course it is. Saying that we don’t know how it copes it isn’t the same as saying that it can’t.

I guess I was trying to emphasize “feeding/reproducing itself”.

Let’s assume for the sake of argument that this critter can’t feed/reproduce itself outside of its symbiotic relationship. Does this affect the minimality of the genome?

Does finding this genome lower the bar, as it were, on the number of genes that would need to be assembled “at random?” Or not, since its a symbiont?

I guess I was trying to emphasize “feeding/reproducing itself”.

I’m assuming it’s an obligate parasite, so it wouldn’t be able to live outside its host. Of course, from a certain point of view, no heterotroph is capable of feeding “itself”, it needs to find food out there to eat. In that respect, parasites are no different than predators, except they get very close and personal with their prey. But being a parasite does provide a very favorable environment and allows them to cast off a lot of stuff that free-living organsisms can’t do without.

It will indeed be interesting to see if it either has co-opted some of the structural proteins produced by the host, or if it actually has somehow transfered portions of its DNA to the host.

really neat.

would love to see a follwup on this in a year or so.

After I read this paper I made a bet with a friend whether it would be idthefuture or uncommondescent who will be the first to claim that this proves abiogenesis must involve 180 genes forming simeltaneously from random nucleotides and is therefore too improbable.

They’ll probably also claim that it’s a wonderful example of “information loss” over time, with only 182 genes. You see, we’re all just cursed, deteriorating specimens descended from “front-loaded”, “heterozygous” perfection.

You see, we’re all just cursed, deteriorating specimens descended from “front-loaded”, “heterozygous” perfection.

a great description of how I view my own aging process from the age of 21 to current.

loaded pefection deteriorating to my current state.

:p

Just to be pedantic for the fun of it, how can we be sure this is in fact the world’s smallest genome, and not just the smallest identified to date? I personally would be astounded if this were the smallest that will ever be found, much less the smallest there really IS, much less the smallest possible.

smallest possible… for what?

That is, 3 Billion base pairs for the human haploid genome.

Flint Wrote:

Just to be pedantic for the fun of it, how can we be sure this is in fact the world’s smallest genome, and not just the smallest identified to date?

We can’t. That’s part of the point here; no one thought they’d ever find a genome even this small, so the idea that the minimally survivable cell must be such and so big is dubious. Life has a way of surprising us.

In my opinion, I think we’ll get to a point where the difference between cell and non-cell becomes ever fuzzier, just as the difference between virus and selfish molecule isn’t so clear-cut either.

I wonder, in trying to figure out a minimum number of genes that could work, is it possible to separate genes needed just for eating and growing, from those needed for dealing with enemies and/or competitors? Presumably a species on very early Earth might have only the inanimate environment to deal with, and if it was in a sheltered location, that might not have been a big problem at the time.

Henry

Ohhh, look at the pretty parasite!

Darn creos! Before I got interested in their special brand of pseudoscience, unfortunately I seldom visited biological sites. I used to think parasites were yuckky - now I find them clever little beasts. I blame Dumbsky for my newfound appreciation of all of evolution.

“the idea that the minimally survivable cell must be such and so big is dubious”

Agreed. Algorithmic information theory, the science that Dumbsky perverts so, seems to tell us that simplicity is in general illdefined. AFAIK there is no general method to construct or test for the simplest construction to perform a specific function. Each suspected case of simplest construction must be compared broadely, probably without finding any method for guarantee.

I don’t know if that follow over to performing several functions. But if we look at a cell as something that performs a finite number of tasks at any time, it looks like a similar difficulty.

Perhaps specific constraints, say of preexisting cellular machinery, helps to narrow such a search. But as I understand it that is probably not the original solution.

On other threads I have been emphasizing the need for logical argument that the man in the street feels comfortable about, based on fact.

As someone who concentrated in his own feeble way on Geology, I invite you to outline in a rigorous manner the likely history of this beasty. When might it have first appeared? How did it at first survive? Have we a cohesion with the history of other, similar forms?

Is it a bacteria - which I assume has DNA - or a virus - without DNA? Or is it a sort of half-and-half? How would the complexity of this organism compare with the very simple organisms knocking about and perhaps helping precipitate iron etc. in early Pre-Cambrian waters?

If Anton shows up, I looked at his reference on the so-called evolutionary improvement of human genetics, and as far as I can see they were simply documenting the usual and expected selective breeding which happens to all species all the time and which keeps them from sudden extinction. I will ask him and anyone else who wishes to comment, is there any observable evidence that higher life-forms are gaining new and improved information in their genetic makeup, this new information being of a category that is demonstrably turning them into a new species? And, is the genetic information carried by higher life-forms being rendered less concise through genetic damage, and is this degeneration being passed on and not eliminated, or have I been hearing things? But is the story for beasties such as the one mentioned on this thread the reverse - i.e., are some micro-organisms improving their genetic prowess in a robust way?

We can talk genomes and that technical side all we wish. It’s mostly lost on the public. It needs to be straightforward. The man in the street knows that if he sees six words strung together in an intelligent sentence, someone wrote it. Evolutionists talk this complex language, but as soon as they get in an argument with a creationist, the creationist asks how six words in a sentence need a creator but six to the power of something “words” in an organism’s genes don’t need a creator. I suggest you re-vamp the approach here. Re-vamp it so you are not saying there is no creator, rather, you are aknowledging that possibility but you are phrasing the science so that the deeper questions aren’t implicit in the science. (That’s what I am attempting at my site.)

PBH: You should not try to make yourself out to be discussing evolution in any sensible manner, nor attempting to “phrasing the science”. You fail miserably, for example here when you show you can’t read a simple text.

Try again to find the words “bacterium” and “DNA” above, that may answer your question about the nature of the beast.

Regards your discussion about accumulating genetic damage, it seems to me from an admittedly cursory reading that you both acknowledge that it is observed to not show up in humans (or perhaps you still hold out the hope that it takes an indefinite time) and try to make it inevitable without any observational support for the latter. It is fun to watch you juggle your cognitive dissonance!

PBH: “or a virus - without DNA”

Forgot this misconception of yours. (Understandably - you have so many.:-) See http://en.wikipedia.org/wiki/Virus for DNA/RNA classifications. Viruses may have both double and single stranded DNA (as for RNA).

Steve Reuland wrote:

In my opinion, I think we’ll get to a point where the difference between cell and non-cell becomes ever fuzzier, just as the difference between virus and selfish molecule isn’t so clear-cut either.

Is this where prions, and the confusion about they-are/they-are-not subject to selection, fit it?

correction: fit in?

is there any observable evidence that higher life-forms are gaining new and improved information in their genetic makeup, this new information being of a category that is demonstrably turning them into a new species?

Yes.

And, is the genetic information carried by higher life-forms being rendered less concise through genetic damage, and is this degeneration being passed on and not eliminated, or have I been hearing things?

So, if the genome is small, creationists will say it’s “loosing information”. If larger, they’ll say it’s either 1) too complex to have evolved and shows evidence of design, or 2) is becoming less concise and “damaged” from a supposed front-loaded state.

Just out of curiosity, how do you determine what is “damaged”? Exactly which genes are damaged? Are you suggesting there is a racial component?

This is encouraging news for synthetic biologists who are hoping to make designer bacteria from scratch…

Steve,

If and when they succeed it would ‘prove’ that life is intelligently designed

Is this where prions, and the confusion about they-are/they-are-not subject to selection, fit it?

I was thinking more about transposons, viroids, etc. But I guess prions would fit the bill too.

Re “Now I understand what removed to the Bathroom Wall means.”

Yeah, it means something got flushed. ;)

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This page contains a single entry by Steve Reuland published on October 13, 2006 11:44 AM.

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